Ok, that's great. Thanks very much for your help. Best wishes and Merry Christmas!
Qi Zhu, PostDoc Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School Herestraat 49, B-3000 Leuven (Belgium) On Wed, Dec 21, 2011 at 7:40 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Yes that is correct. That was fixed with version 5.1 so current > distributions do the right thing. > doug > > > Qi Zhu wrote: >> >> Yes, seems weird. The image that I attached to you in the first mail >> is actually a t map, so the t value in those areas are also zero. >> And according to what I read from fast_selxavg3.m, the t value is >> actually calculated from the fsig, which is: t.vol = >> sqrt(fsig.vol).*sign(ces.vol), and fsig.vol is calculated from the p >> value that came from the Ftest. So the t value is calculated wrong in >> fs 5.0. >> I am now changing this line to: >> >> Fvol = fast_mat2vol(Fmat,mri.volsize); >> t.vol = sqrt(Fvol).*sign(ces.vol); >> >> Is this correct? >> >> Best, >> >> Qi Zhu, PostDoc >> Laboratorium voor Neuro- en Psychofysiologie >> K.U.Leuven Medical School >> Herestraat 49, B-3000 Leuven (Belgium) >> >> On Wed, Dec 21, 2011 at 5:31 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu> wrote: >> >>> >>> The t is computed as the signed square root of the F (not Fsig) volume: >>> >>> t.vol = sqrt(Fvol.vol) .* sign(ces.vol); >>> >>> The Fvol (and do t) is not computed from the sig (the other way around). >>> Are >>> you sure that the t-value does not look right in those areas? >>> >>> doug >>> >>> >>> >>> Qi Zhu wrote: >>> >>>> >>>> Dear Doug, >>>> >>>> Thanks very much for your prompt response. I tried what you suggested >>>> and the sig map looks fine now, that's probably the best that we can >>>> get for the sig map, because of the limitation of the MATLAB I guess. >>>> But for the t map, the values are still not correct for those voxels >>>> that highly activated, because they're just calculated based on the >>>> sig values, and they can only go up to 17.98 in my case because of the >>>> limitation. And I am also quite confused by the way that selxavg3 >>>> calculated the t values, which are calculated as the square root of >>>> Fsig values, but not the F values. Is that correct? >>>> >>>> Best, >>>> >>>> Qi Zhu, PostDoc >>>> Laboratorium voor Neuro- en Psychofysiologie >>>> K.U.Leuven Medical School >>>> Herestraat 49, B-3000 Leuven (Belgium) >>>> phone +32 16 33 02 09 >>>> >>>> On Tue, Dec 20, 2011 at 8:54 PM, Douglas N Greve >>>> <gr...@nmr.mgh.harvard.edu> wrote: >>>> >>>> >>>>> >>>>> I think this is due to the high DOF and probably high t-value causing >>>>> the >>>>> significance in matlab to be computed as 0. This gets converted to Inf >>>>> (infinity) when the -log10(p) calculation is made, then the Inf gets >>>>> set >>>>> to >>>>> 0 when the volume is saved. The quick fix for you is to change >>>>> fast_selxavg3.m (in $FREESURFER_HOME/fsfast/toolbox). There is a single >>>>> line >>>>> that reads: >>>>> >>>>> fsigmat = -log10(pmat) >>>>> >>>>> change this to >>>>> >>>>> fsigmat = -log10(pmat + eps(0)); >>>>> >>>>> Let me know if this works and I'll update our source code. >>>>> >>>>> doug >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Qi Zhu wrote: >>>>> >>>>> >>>>>> >>>>>> Dear Doug, >>>>>> >>>>>> I used selxavg3-sess in freesurfer 5.0 to run a big GLM analysis on a >>>>>> monkey data set containing 147 runs. But When I check the results, I >>>>>> found that in the voxels where the t-values should be very high were >>>>>> turned out to have a value of zero. I checked the brainmask, the ces >>>>>> and the cesvar values, they all look fine. It seems that only the ces >>>>>> values in these voxels are a bit high compared to the nearby normal >>>>>> voxels (e.g. 1.17 (ces)/0.00048(cesvar) compared to 0.74/0.00040 in a >>>>>> nearby normal voxel). And it seems that not only me have this problem >>>>>> (similar problem posted in the mailinglist before. >>>>>> >>>>>> >>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13789.html). >>>>>> Do you know what the problem would be and how to solve it? Thanks very >>>>>> much for your help. >>>>>> >>>>>> Attached please find an image of the problem. >>>>>> >>>>>> Best, >>>>>> >>>>>> Qi Zhu, PostDoc >>>>>> Laboratorium voor Neuro- en Psychofysiologie >>>>>> K.U.Leuven Medical School >>>>>> Herestraat 49, B-3000 Leuven (Belgium) >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom >>>>> it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>> in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >> >> >> >> > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
